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- PDB-5fxd: Crystal structure of eugenol oxidase in complex with isoeugenol -

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Basic information

Entry
Database: PDB / ID: 5fxd
TitleCrystal structure of eugenol oxidase in complex with isoeugenol
ComponentsPROBABLE VANILLYL-ALCOHOL OXIDASE
KeywordsOXIDOREDUCTASE / BIOCATALYSIS / SELECTIVE OXIDATION / KINETIC RESOLUTION / OXIDASES / EUGENOL
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / D-lactate dehydrogenase (NAD+) activity / FAD binding / metal ion binding
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 ...Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / ISOEUGENOL / Probable vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesRHODOCOCCUS JOSTII RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNguyen, Q.-T. / de Gonzalo, G. / Binda, C. / Martinez, A.R. / Mattevi, A. / Fraaije, M.W.
CitationJournal: Chembiochem / Year: 2016
Title: Biocatalytic Properties and Structural Analysis of Eugenol Oxidase from Rhodococcus Jostii Rha1: A Versatile Oxidative Biocatalyst.
Authors: Nguyen, Q. / De Gonzalo, G. / Binda, C. / Rioz-Martinez, A. / Mattevi, A. / Fraaije, M.W.
History
DepositionMar 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE VANILLYL-ALCOHOL OXIDASE
B: PROBABLE VANILLYL-ALCOHOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4687
Polymers117,4772
Non-polymers1,9925
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-71.3 kcal/mol
Surface area33880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.720, 96.690, 179.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999, 0.02864, -0.03305), (0.03649, 0.1296, -0.9909), (-0.0241, -0.9912, -0.1305)
Vector: 13.51, 25.38, 29.3)

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Components

#1: Protein PROBABLE VANILLYL-ALCOHOL OXIDASE / EUGENOL OXIDASE


Mass: 58738.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT BOND BETWEEN THE FAD AND HIS390 / Source: (gene. exp.) RHODOCOCCUS JOSTII RHA1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q0SBK1
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-H7Y / ISOEUGENOL


Mass: 164.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsFLAVIN-ADENINE DINUCLEOTIDE (FAD): COVALENT BOND BETWEEN FAD AND HIS390
Sequence detailsOTHER DETAILS THIS RESEARCH WAS SUPPORTED THE EUROPEAN UNION (EU) PROJECT ROBOX (GRANT AGREEMENT NO. ...OTHER DETAILS THIS RESEARCH WAS SUPPORTED THE EUROPEAN UNION (EU) PROJECT ROBOX (GRANT AGREEMENT NO. 635734) UNDER EU'S HORIZON 2020 PROGRAMME RESEARCH AND INNOVATION ACTIONS H2020-LEIT BIO-2014-1.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 8 / Details: 24% PEG6000, 0.1 M TRIS/HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98
DetectorType: PILATUS / Detector: PIXEL / Date: Aug 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→85 Å / Num. obs: 109694 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.8 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VAO

2vao


Resolution: 1.7→89.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.405 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19881 5370 4.9 %RANDOM
Rwork0.15982 ---
obs0.16172 104195 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→89.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 136 627 9008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198606
X-RAY DIFFRACTIONr_bond_other_d0.0020.027973
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.97911689
X-RAY DIFFRACTIONr_angle_other_deg1.134318350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51251048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70124.063411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.199151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1481558
X-RAY DIFFRACTIONr_chiral_restr0.1270.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219812
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022000
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6811.7024198
X-RAY DIFFRACTIONr_mcbond_other1.6811.7024197
X-RAY DIFFRACTIONr_mcangle_it2.322.5475244
X-RAY DIFFRACTIONr_mcangle_other2.3192.5475245
X-RAY DIFFRACTIONr_scbond_it3.0682.0394408
X-RAY DIFFRACTIONr_scbond_other3.0682.0394408
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6142.9246446
X-RAY DIFFRACTIONr_long_range_B_refined5.63714.67410552
X-RAY DIFFRACTIONr_long_range_B_other5.63714.67410552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 370 -
Rwork0.259 7597 -
obs--98.27 %

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